“You aren’t stupid, are you?” “Yes.”

In English, the answer to a yes/no question does not change if the question becomes negative.

So the answer to these three questions should be the same:

Are you stupid?	No, I’m not.
You’re stupid, aren’t you?	No, I’m not.
You aren’t stupid, are you?	No, I’m not.

Examples

Wrong	Right
“You’re not stupid, are you? “Yes, I’m not.”	“You’re not stupid, are you? “No, I’m not.”
“You’re not a monkey, are you?” “Yes, I’m not.”	“You’re not a monkey, are you?” “No, I’m not.”
“You didn’t eat my cake, did you?” “Yes, I didn’t.”	“You didn’t eat my cake, did you?” “No, I didn’t.”
“You weren’t reading that, were you?” “No, I was.”	“You weren’t reading that, were you?” “Yes, I was.”